Xinzhu Zhou

Publication Date


Document Type

Honors Project


Biological Sciences


Genetics, Evolutionary genetics, Ciliates-Genetics, Bioinformatics, Genome evolution, Ciliates


A single-celled ciliate, Chilodonella uncinata is an emerging model species for understanding genome evolution in eukaryotes. Analogous to the germline-soma distinction in other eukaryotes, the two nuclei in C. uncinata separate genetic material for the soma from that for sex. The somatic macronucleus (MAC) is the site of transcirption of protein coding genes, while the germline micronucleus (MIC) is transcriptionally silenced. Nuclear dimorphism allows C. uncinata to rearrange genome structure extensively. Through a genome rearrangement mechanism termed alternative processing, one transcript of MIC generates a rich repertoire of gene families. The present study set out to find alternatively processed gene families in two lineages of C. uncinata, the correlation between GC content and codon usage, conservation pattern inUTRs, and conserved motif in internal intron sequences of C. uncinata. Computational results showed the K antiporter p-type alpha subunit family protein, cathepsin b, and a/b hydrolase associated lipase region family are candidate alternatively processed gene families in C. uncinata. The effective number of codons used by putative open reading frames (ORFs) in C. uncinata did not seem to be correlated with the base composition of the ORFS, a finding that suggests that selection for a particular effective number of codons could override background mutations in C. uncinata. Lastly, we could not identify conserved motif in 3'UTRS and internal intron sequences in C. uncinata, while we found one conserved motif in 5'UTRS, which suggests that conserved motif in non-coding regions in single-celled protists might be organism-specific.




76 pages : color illustrations. Honors Project-Smith College, 2014. Includes bibliographical references (pages 48-52)